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I love how you listed different theories for a concrete case. This is exactly what this community needs more of.
This might be helpful.
First, anti histamines has effects on eyes. They can cause angle closure glaucoma attacks, and they cause dry eyes. Dry eyes with contact lenses causes distortions and the eyes have to work way harder. Especially if combined with any allergies. I 100% get eye pain from some types of anti histamines, and should probably look into it some more.
What contacts do you use? It has a big effect. Look into spherical vs aspherical. Try both. They look entirely different in the dark with astigmatism. If you use Acuvue Oasis that is popular there is a ton of reddit posts on people that got massive issues after they changed to the green packaging. I started having issues when that switch happened, and I decided to try the Max version with shitty green tint. Not necessarily related, but do check.
Ofc you have the possibility that something started using another neural pathway while doing something uncommon like the Kindle display. Neurons that fire together wire together and all that. Some of this stuff related to visual pathways is crazy advanced and hard to get a grip on.
If you use displays that are plugged in to the power grid make sure you don't plug a bunch of other new thins into the same multi-plug extension cord. I've seen one computer refuse to start, and a screen overheat, just from being in an extension cord with other things.
Also make sure there are no changes to your light setup. From my experience introducing another flicker at another frequency can cause havoc. Bulbs can also go bad after a while. The easiest way to check is the slow motion camera on your mobile.